If you consult an acupuncturist, you probably believe that no harm will come to you. Most people see complementary medicine as natural, and all things natural are assumed to be safe. Challenging this deeply ingrained concept sometimes seems like slaughtering a holy cow. Safety is too important an issue to be left to self-interested assumptions. Surely, evidence is mandatory. So, about 10 years ago, I decided to systematically investigate the safety of complementary therapies, including acupuncture. I vividly remember the uproar this caused. Threats, lawyers' letters, hate mail: you name it, I had it. How did I dare? Who did I think I was ?

Needless to say that, with a few exceptions, the practitioners were less than cooperative. But my allegiance must be to the patient, as well as to good science, and not necessarily to practitioners. My team proceeded to publish a series of articles demonstrating that acupuncture is by no means free of risks. In fact, numerous, quite horrendous complications had been reported: needles penetrating internal organs such as the heart, lung or spine; needles introducing infections such as hepatitis; some patients had even died. Acupuncturists were, of course, adamant that these were exotically rare instances, flukes with no relevance to their practice. Again, I argued that facts are preferable to assumptions.

Eventually we conducted the acid test. The idea was to monitor a large number of patients and determine exactly how often complications happened. To reach the numbers needed for a meaningful result, we tried to work with the large group of acupuncturists who are not medically trained - they like to call themselves "professional acupuncturists" - as opposed to "medical acupuncturists" who have studied medicine. You can probably guess what happened next: first, they didn't see the point of such a study, and when they did they were petrified at the thought of cooperating with us. What if the findings were less than reassuring? After lengthy discussions, the professional acupuncturists decided to appropriate most of our "know-how", refuse collaboration, and conduct their own study.

As it turned out, this was a very good thing. It meant that not one but two large studies got under way. Each included around 30,000 consultations with acupuncturists of different backgrounds. The results were in perfect agreement: adverse effects occurred in 7% of all cases - not a negligible figure - but side-effects were reassuringly mild and of short duration: pain, minor bleeding, drowsiness. No serious adverse effects were noted.

Inspired by these investigations, we teamed up with German researchers to analyse an even larger sample. It included almost 100,000 patients treated by medical acupuncturists; the results were published earlier this year. Again we found minor adverse events in about 7% of cases.

The last episode in this odyssey towards establishing the safety of acupuncture is a brand new report published in Quality and Safety of Health Care. It involved 638 acupuncturists registered with the British Acupuncture Council. Their patients completed questionnaires on adverse effects three months after treatment. A total of about 30,000 consultations were included. The rate of side-effects turned out to be 11%. Once again, few serious adverse effects were noted. Again, a reassuring result - or is it? Three per cent of all patients reported that their acupuncturist advised them to reduce or stop medications, including essential ones such as heart drugs prescribed by their doctor. If followed, such a recommendation could easily endanger a life.

In any case, the holy cow, it seems, has been resuscitated. Based on prospective studies of almost 200,000 consultations, we are now able to state for the first time in its long history that acupuncture is reasonably safe. Safer than regularly taking aspirin, for instance. Acupuncturists would reply that they knew this all the time. Not true. They assumed it all the time, and that's a big difference.

For me, this crusade is one of the most revealing stories in my entire research career, a story with a moral: investigating controversial subjects that are uncomfortably sensitive and unpopular with proponents of complementary medicine is not necessarily a bad thing. In the final analysis, it can only help complementary medicine. And the truth will always benefit patients.

· Edzard Ernst is professor of complementary medicine at the Peninsula Medicine School at the universities of Exeter and Plymouth.